[gmx-users] The solvation free energy of a vdw ligand

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 17 16:14:43 CET 2012

Tanping Li wrote:
> Dear all,
> I posted the message yesterday and haven't get a response. My trouble is that: when I calculate the solvation free energy of a vdw ligand, the energy of lambda=0 varies with different state B. 
> Does anyone has the similar experience? I greatly appreciate your help since I tried a lot but haven't find the reason.

Version 3.3.1 is ancient, and there may well be a bug that has since been fixed 
in the intervening years.  Try again with version 4.5.5 (though there are 
significant changes in the way the free energy code works, it should not affect 
the simple test you've proposed).


> Yours
> Tanping     
> --- On Thu, 2/16/12, Tanping Li <jia_11_osu at yahoo.com> wrote:
>> From: Tanping Li <jia_11_osu at yahoo.com>
>> Subject: [gmx-users] The free energy of vdw part
>> To: gmx-users at gromacs.org
>> Date: Thursday, February 16, 2012, 11:28 AM
>> Dear gmx users,
>> I am calculating the free energy of solvating a small ligand
>> by water, using FEP method. The free energy is separated
>> into the contribution of electric+vdw. I find problem for
>> the vdw part.
>> I am using gromacs-3.3.1. In the top file, I set the state B
>> of ligand where LJ parameters of atoms are zero; in the mdp
>> file, I set the lamda=0.
>> According to my understanding, above setting should gives me
>> the energy of ligand's state A. However, when I calculate
>> the energy with a mdp with "free_energy=No" and a top
>> without setting the B state, I get a very different energy.
>> I tried but haven't dig out which part I missed. I greatly
>> appreciate your help and consideration on this issue.
>> -- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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